how to get molecular weight

[srio]

Hello Tom,

I came to a problem: using the compound parser I cannot get the molecular weight of the compound. The compound information should have either the final molecular weight or the number of different elements (to be able to compute it). For example, with H2O:

In [106]: xraylib.CompoundParser("H2O") Out[106]: {'Elements': [1, 8], 'massFractions': [0.1120976692563818, 0.8879023307436182], 'nAtomsAll': 3.0, 'nElements': 2}

How I can get the molecular weight = 2_xraylib.AtomicWeight(1) + 1_xraylib.AtomicWeight(8) ?

If it is not possible, please consider it for a future version!!

Thanks a lot,

Manolo

[tschoonj]

Hi Manolo,

This is currently not calculated by the compound parser.

I will look into it. Shouldn't be hard to implement.

Best,

Tom

[srio]

Thanks. I think is important to store the number of atoms of each element, so in water [2,1] for Z=[1,8]. With this and AtomicWeight() we can survive. Many thanks for your quick answer!! M

On 06/21/2016 04:15 PM, Tom Schoonjans wrote:

Hi Manolo,

This is currently not calculated by the compound parser.

I will look into it. Shouldn't be hard to implement.

Best,

Tom

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[tschoonj]

Hi Manolo,

I am currently working on this and work should be finished soon.

Just to be clear (I had to use wikipedia for this...): you are referring to molar mass right (in g/mol)? Molecular mass is the mass of a particular molecule and varies according to isotopes present in it and (currently) cannot be provided by xraylib.

Best,

Tom

[srio]

Thanks Tom. Yes you are right is the molar mass (or molecular mass for "averaged" isotopes). I never paid attention to the names...

Best regards,

Manolo

On 07/06/2016 03:03 PM, Tom Schoonjans wrote:

Hi Manolo,

I am currently working on this and work should be finished soon.

Just to be clear (I had to use wikipedia https://en.wikipedia.org/wiki/Molar_mass for this...): you are referring to /molar mass/ right (in g/mol)? /Molecular mass/ is the mass of a particular molecule and varies according to isotopes present in it and (currently) cannot be provided by xraylib.

Best,

Tom

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[tschoonj]

Hi Manolo,

I have changed the compoundData struct according to your requirements. It now contains nAtoms, an array of double's with the number of atoms per element, and molarMass, the molar mass of the compound, in g/mol.

As I have no immediate plans to make a new release, I recommend you clone the repo if you want the new compoundData struct.

Best,

Tom

[srio]

Thanks a lot Tom.

I'm trying to reinstall xraylib. One question (I already got your answer but do not remember). How I create the "configure" script that is not present in github? (I usually download xraylib from http://lvserver.ugent.be/xraylib/xraylib-3.1.0.tar.gz )

Thanks a lot!!

Manolo

On 07/06/2016 03:03 PM, Tom Schoonjans wrote:

Hi Manolo,

I am currently working on this and work should be finished soon.

Just to be clear (I had to use wikipedia https://en.wikipedia.org/wiki/Molar_mass for this...): you are referring to /molar mass/ right (in g/mol)? /Molecular mass/ is the mass of a particular molecule and varies according to isotopes present in it and (currently) cannot be provided by xraylib.

Best,

Tom

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Manuel Sanchez del Rio European Synchrotron Radiation Facility BP 220, 38043 Grenoble-Cedex 9 (France) email: srio@esrf.eu Tel +33-476 882513 Fax +33-476 882542 http://www.esrf.eu

[tschoonj]

autoreconf -i

[srio]

Thanks Tom. I get some errors, any hint? :

First error (ubuntu 14.04):

chac:~/Oasys/OASYS_VE/xraylib % autoreconf -i configure.ac:45: error: possibly undefined macro: AC_PROG_LIBTOOL If this token and others are legitimate, please use m4_pattern_allow. See the Autoconf documentation. autoreconf: /usr/bin/autoconf failed with exit status: 1

I do it again:

chac:~/Oasys/OASYS_VE/xraylib % autoreconf -i configure.ac:39: installing 'build-aux/ar-lib' configure.ac:33: installing 'build-aux/compile' configure.ac:19: installing 'build-aux/config.guess' configure.ac:19: installing 'build-aux/config.sub' configure.ac:18: installing 'build-aux/install-sh' configure.ac:18: installing 'build-aux/missing' example/Makefile.am: installing 'build-aux/depcomp' parallel-tests: installing 'build-aux/test-driver' fortran/Makefile.am:17: error: Libtool library used but 'LIBTOOL' is undefined fortran/Makefile.am:17: The usual way to define 'LIBTOOL' is to add 'LT_INIT' fortran/Makefile.am:17: to 'configure.ac' and run 'aclocal' and 'autoconf' again. fortran/Makefile.am:17: If 'LT_INIT' is in 'configure.ac', make sure fortran/Makefile.am:17: its definition is in aclocal's search path. idl/Makefile.am:25: error: Libtool library used but 'LIBTOOL' is undefined idl/Makefile.am:25: The usual way to define 'LIBTOOL' is to add 'LT_INIT' idl/Makefile.am:25: to 'configure.ac' and run 'aclocal' and 'autoconf' again. idl/Makefile.am:25: If 'LT_INIT' is in 'configure.ac', make sure idl/Makefile.am:25: its definition is in aclocal's search path. lua/Makefile.am:15: error: Libtool library used but 'LIBTOOL' is undefined lua/Makefile.am:15: The usual way to define 'LIBTOOL' is to add 'LT_INIT' lua/Makefile.am:15: to 'configure.ac' and run 'aclocal' and 'autoconf' again. lua/Makefile.am:15: If 'LT_INIT' is in 'configure.ac', make sure lua/Makefile.am:15: its definition is in aclocal's search path. perl/Makefile.am:16: error: Libtool library used but 'LIBTOOL' is undefined perl/Makefile.am:16: The usual way to define 'LIBTOOL' is to add 'LT_INIT' perl/Makefile.am:16: to 'configure.ac' and run 'aclocal' and 'autoconf' again. perl/Makefile.am:16: If 'LT_INIT' is in 'configure.ac', make sure perl/Makefile.am:16: its definition is in aclocal's search path. php/Makefile.am:15: error: Libtool library used but 'LIBTOOL' is undefined php/Makefile.am:15: The usual way to define 'LIBTOOL' is to add 'LT_INIT' php/Makefile.am:15: to 'configure.ac' and run 'aclocal' and 'autoconf' again. php/Makefile.am:15: If 'LT_INIT' is in 'configure.ac', make sure php/Makefile.am:15: its definition is in aclocal's search path. python/Makefile.am:17: error: Libtool library used but 'LIBTOOL' is undefined python/Makefile.am:17: The usual way to define 'LIBTOOL' is to add 'LT_INIT' python/Makefile.am:17: to 'configure.ac' and run 'aclocal' and 'autoconf' again. python/Makefile.am:17: If 'LT_INIT' is in 'configure.ac', make sure python/Makefile.am:17: its definition is in aclocal's search path. python/Makefile.am:27: installing 'build-aux/py-compile' ruby/Makefile.am:15: error: Libtool library used but 'LIBTOOL' is undefined ruby/Makefile.am:15: The usual way to define 'LIBTOOL' is to add 'LT_INIT' ruby/Makefile.am:15: to 'configure.ac' and run 'aclocal' and 'autoconf' again. ruby/Makefile.am:15: If 'LT_INIT' is in 'configure.ac', make sure ruby/Makefile.am:15: its definition is in aclocal's search path. src/Makefile.am:20: error: Libtool library used but 'LIBTOOL' is undefined src/Makefile.am:20: The usual way to define 'LIBTOOL' is to add 'LT_INIT' src/Makefile.am:20: to 'configure.ac' and run 'aclocal' and 'autoconf' again. src/Makefile.am:20: If 'LT_INIT' is in 'configure.ac', make sure src/Makefile.am:20: its definition is in aclocal's search path. autoreconf: automake failed with exit status: 1

Now trying configure:

chac:~/Oasys/OASYS_VE/xraylib % ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define EXTENSIONS... yes checking for strndup... yes checking for strdup... yes checking for ar... ar checking the archiver (ar) interface... ar ./configure: line 5085: syntax error near unexpected token 2.0.0' ./configure: line 5085:LT_PREREQ(2.0.0)'

On 07/07/2016 04:32 PM, Tom Schoonjans wrote:

|autoreconf -i|

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[tschoonj]

You have to install libtool first with apt-get

[srio]

Got it. I need to install (ubuntu 14.04):

On 07/07/2016 04:32 PM, Tom Schoonjans wrote:

|autoreconf -i|

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Manuel Sanchez del Rio European Synchrotron Radiation Facility BP 220, 38043 Grenoble-Cedex 9 (France) email: srio@esrf.eu Tel +33-476 882513 Fax +33-476 882542 http://www.esrf.eu

[srio]

It works! Beautiful, thanks a lot.

On 07/07/2016 04:51 PM, Tom Schoonjans wrote:

You have to install |libtool| first with |apt-get|

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Manuel Sanchez del Rio European Synchrotron Radiation Facility BP 220, 38043 Grenoble-Cedex 9 (France) email: srio@esrf.eu Tel +33-476 882513 Fax +33-476 882542 http://www.esrf.eu